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"What's the matter? All I said was that Komaytos look like little Metr—" Non-canon warning: This article or section contains information that may not be considered an official part of the Metroid series in the overall storyline by Nintendo.

The comic begins with Samus landing on the Frigate Orpheon and beginning to explore. She comes across an unnamed worm-like creature (presumably an experiment specimen), heavily wounded Space Pirates, a Metroid and the Parasite Queen. After she defeats the latter, the station begins to explode. Just before Samus can make it back to her gunship, her suit is damaged by a random power surge, reverting it to her Power Suit.

"Over 10 hours" later, Samus enters the Artifact Temple. She mentions that she worried that her suit would not work as well in the Impact Crater, but that she was lucky to find the Phazon Suit upgrade. She prepares to open the seal to enter the crater, but then Meta Ridley attacks and destroys the totems. She incinerates him with her Flamethrower and continues on.

When she enters the crater, she soon encounters the Metroid Prime and battles it, destroying its exoskeleton and forcing the core essence of the creature to engage Samus in its true form. It creates a pool of Phazon and spawns Fission Metroids, which Samus destroys with a Power Bomb. She then discovers that the pool of Phazon charges her suit, allowing her to use the Phazon Beam to destroy the Metroid Prime. This overloads her Phazon Suit and reverts it to her Gravity Suit. She then escapes the crater and stands atop her ship, her helmet removed.

Samus, for instance, exclaims that Zebes was destroyed two years prior (although she might have been referring to the base), while no time frame was given in the original release and was later confirmed in the art booklet to be three years. She also expresses surprise in seeing a live Metroid aboard the Orpheon, which again implies at this version taking place after the events of Super Metroid rather than the original Metroid. In-game scans do show that Metroids were there at one point, but moved by the time the Bounty Hunter arrived.

She also killed the Parasite Queen in a significantly different manner, firing a missile at an Ionized Nitrogenic Coolant Tank near the Queen's tank instead of shooting at the queen herself via gaps in the reactor's shielding.

On a related note, the Parasite Queen was given a different design than her in-game appearance.

In addition, the ending of the first issue implies that Samus lost her Varia Suit alongside most of her weapons and equipment barring her power beam and her power suit after she barely boarded her gunship, when in-game she lost them due to being caught inside a power surge near an elevator terminal.

Meta Ridley lacks his trademark head-crest and is easily defeated by the Flamethrower, despite being practically resistant to the weapon in-game, and was also actually defeated by the Chozo Statues in the temple and not by Samus.

Samus also mentions that she was able to find the Phazon Suit as an upgrade, while in-game it was created by viral corruption due to the Omega Pirate's corpse falling on her and covering her in Phazon.

When entering the Impact Crater, Samus says "whatever secrets the Space Pirates are hiding lie inside." while only the NTSC version of the game depicted the Pirates entering the crater.

When Samus defeats Metroid Prime, she mentions that her Phazon Suit was overloaded and then reverted to the Gravity Suit, while in-game, Metroid Prime absorbed the Phazon Suit to survive.

Finally, at the end of the comic Samus stands atop her gunship with her helmet off and hair loose and flying in the wind, while in-game it is tied back into a ponytail and it hardly billows.

The hint of Metroid Prime's survival from the complete ending is missing.